In wallace: A Modular Platform for Reproducible Modeling of Species Niches and Distributions

```{asis, echo = {{envs_worldclim_knit}}, eval = {{envs_worldclim_knit}}, include = {{envs_worldclim_knit}}}

Obtain environmental data

Using WorldClim v2.1 (http://www.worldclim.org/) bioclimatic dataset at resolution of r {{wcRes_rmd}} arcmin.

```r}, include = {{envs_worldclim_knit}}}
# Download environmental data 
envs_{{spAbr}} <- envs_worldclim(
  bcRes = {{wcRes_rmd}}, 
  bcSel = {{bcSel_rmd}}, 
  mapCntr = {{mapCntr_rmd}}, # Mandatory for 30 arcsec resolution   
  doBrick = {{wcBrick_rmd}})
occs_xy_{{spAbr}} <- occs_{{spAbr}}[c('longitude', 'latitude')]
occs_vals_{{spAbr}} <- as.data.frame(raster::extract(envs_{{spAbr}}, occs_xy_{{spAbr}}, cellnumbers = TRUE))
# Remove duplicated same cell values
occs_{{spAbr}} <- occs_{{spAbr}}[!duplicated(occs_vals_{{spAbr}}[, 1]), ]
occs_vals_{{spAbr}} <- occs_vals_{{spAbr}}[!duplicated(occs_vals_{{spAbr}}[, 1]), -1]
# remove occurrence records with NA environmental values
occs_{{spAbr}} <- occs_{{spAbr}}[!(rowSums(is.na(occs_vals_{{spAbr}})) >= 1), ]
# also remove variable value rows with NA environmental values
occs_vals_{{spAbr}} <- na.omit(occs_vals_{{spAbr}})
# add columns for env variable values for each occurrence record
occs_{{spAbr}} <- cbind(occs_{{spAbr}}, occs_vals_{{spAbr}})

wallace documentation built on Sept. 11, 2024, 9:16 p.m.